Okay - well the new API will be ideal for the profiling of lots of tables. In fact we had a guy in our team demonstrate that to us - we had a customer who complained that he had thousands of tables to profile... You should check it out and if you need some guidance let me know. There's even an API client to help you on the way, but I might be able to get some sample code to you too.
The new API Client details
here. Version 5.2.3 is the latest release.
I have seen the UI slow down with lots of tables (especially wide ones), we build an internal table so it takes some time... but I am not aware of the exact limitations.
Good luck with your project.
Gary